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Abstract:

Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis at atomic resolution remains ambiguous. The three dimensional structure of protein is not always adequate to provide a complete understanding of protein function. We use atomistic molecular dynamics simulations to complement experiments to understand how protein conformational dynamics are coupled to allosteric function. We analyze multi-dimensional simulation trajectories by mapping key dynamical features within individual macrostates as residue-residue contacts. In this talk, we will discuss computational studies on members of a ubiquitous family of enzymes that regulate many sub-cellular processes. The effects of distal mutations and substrate binding are observed at locations far beyond the mutation and binding sites, implying their importance in allostery. The results provide insights into the general interplay between enzyme conformational dynamics and catalysis from an atomistic perspective that have implications for structure based drug design and protein engineering.

Abstract:

Polymerizing monomers into periodic two-dimensional (2D) networks provides structurally precise, layered macromolecular sheets that exhibit desirable mechanical, optoelectrotronic, and molecular transport properties. 2D covalent organic frameworks (COFs) offer broad monomer scope but are generally isolated as powders comprised of aggregated nanometer-scale crystallites. I will discuss 2D COF formation using a two-step procedure, in which monomers are added slowly to pre-formed nanoparticle seeds. The resulting 2D COFs are isolated as single-crystalline, micron-sized particles. Transient absorption spectroscopy of the dispersed COF nanoparticles provides two to three orders of magnitude improvement in signal quality relative to polycrystalline powder samples and suggests exciton diffusion over longer length scales than those obtained through previous approaches. These findings will enable a broad exploration of synthetic 2D polymer structures and properties.

ABSTRACT: What are the thermodynamic driving forces that influence the free energy of membrane protein folding and association in lipid bilayers? For soluble proteins, the burial of hydrophobic groups away from aqueous interfaces is a major driving force, but membrane-embedded proteins cannot experience hydrophobic forces, as the lipid bilayer lacks water. A fundamental conundrum thus arises: how does a greasy protein surface find its greasy protein partner in the greasy lipid bilayer to fold faithfully into its native structure? Recently, a structurally stable and functional monomeric form of the normally homodimeric Cl^-/H⁺ antiporter CLC-ec1 was designed by introducing tryptophan mutations at the dimer interface. We have used this to develop a new model system for studying reversible dimerization in membranes for free energy measurements, which encompasses the thermodynamic properties of protein interactions in the membrane environment. To quantify monomer vs. dimer populations across a wide range of protein densities, we developed a method that quantifies the capture of subunits into liposomes from large equilibrium membranes single-molecule photobleaching by total internal reflection microscopy.  With this, we are able to determine that CLC-ec1 has a free energy of dimerization of -11 kcal/mole in 2:1 POPE/POPG membranes.  We are now investigating why this complex is so stable, dissecting the changes in enthalpy and entropy while varying protein interactions or the composition of the lipid solvent.  The results from this study will provide a physical foundation for the development of informed strategies aimed at correcting protein mis-folding or regulating protein interactions in membranes in physiologically and pathological situations.

Abstract:

Size-selective cryogenic photoelectron spectroscopy (cryoPES) coupled with electrospray ionization source (ESI) has been demonstrated to be a powerful experimental technique to investigate electronic structures and energetics of a wide variety of solution phase species and chemistry in the gas phase. In this talk, I will present the latest results probing various novel molecular clusters ranged from closo-dodecaborate dianions [B₁₂X₁₂]^2- to atmospherically relevant species by employing this technique. Transition state dynamics of unimolecular isomerization and chemical reactions via photodetachment of corresponding precursor anions will be reported as well. Future directions of ESI-cryoPES, leading to high resolution photoelectron imaging spectroscopy and time-resolved pump-probe experiments will also be briefly discussed.

Abstract:

Magnetic particle imaging (MPI) is an emerging imaging modality that enables the direct mapping of iron oxide nanoparticle tracers.  In MPI, the development of tailored magnetic nanoparticle tracers is paramount to achieving high sensitivity and good spatial resolution. This talk will provide a general overview of the progress in MPI tracer development over the past decade, and will also focus on emerging directions and new opportunities for iron oxide-based tracer design and applications. The presentation will cover magnetic nanoparticle relaxation in MPI and discuss key aspects to consider in tailoring tracers for MPI applications. Emphasis will be given on how structural changes (size, composition, shape, surface chemistry) and inter-particle interactions affect the MPI signal generation process. Moreover, the presentation will discuss emerging research directions in color-MPI (cMPI) and MPI-guided hyperthermia (hMPI).

Abstract

Lignin remains one of the most significant barriers to the efficient utilization of lignocellulosic substrates, in processes ranging from ruminant digestibility to indus­trial pulping, and in the current focus on biofuels production. Inspired largely by the recalcitrance of lignin to biomass processing, plant en­gineering has routinely sought to alter lignin quantity, composition, and structure by exploiting the inherent plasticity of lignin biosynthesis.



More recently, researchers are attempting to strategically design plants for increased degradability by incorporating monomers that lead to a lower degree of polymerization, reduced hydrophobicity, fewer bonds to other cell wall constituents, or novel chemically labile linkages in the polymer backbone.1,2 The incorporation of value-added structures could also help valorize lignin. Designer lignins may satisfy the biological requirement for lignification in plants while improving the overall efficiency of biomass utilization. Although possibilities abound, maintaining plant health is paramount and, ultimately, the plants themselves will dictate which of these approaches can be tolerated.



One such method, via the so-called ‘zip-lignin’ approach, is showing particular promise.3-5 Poplar has been engineered to incorporate monolignol ferulate conjugates into the lignification process, by using an exotic transferase gene, FMT, and a xylem-specific promoter.5 This results in the introduction of readily cleavable ester linkages into the backbone of the polymer, and delivers significantly improved processing. Various applications for which these altered trees appear superior are only just beginning to be explored. Now that we have sensitive methods for determining if/when/whether plants are making monolignol ferulate conjugates and using them for lignification, it appears that Nature herself may have already been exploring this avenue.6 In attempting to modify monocot lignins, another transferase appears to be useful for improving cell wall digestibility. This involves p-coumaroylation of the lignin. Although this occurs naturally in monocots, it is not evident in dicots, but providing dicots with that pathway has interesting implications.7,8

Nature continues to inspire us with new avenues toward lignin modification that have potential value for various processes. For example, the ramifications of finding that grasses are using tricin, a flavone from beyond the monolignol biosynthetic pathway, to start lignin chains are interesting; tricin itself is valuable, and plants with tricin knocked out have higher lignin and lower CW digestibility.9-13 

1.    Mottiar Y, Vanholme R, Boerjan W, Ralph J, & Mansfield SD (2016) Designer lignins: harnessing the plasticity of lignification. Current Opinion in Biotechnology 37(1):190-200.



2.    Rinaldi R, Jastrzebshi R, Clough MT, Ralph J, Kennema M, Bruijnincx PCA, & Weckhuysen BM (2016) Paving the way for lignin valorisation: Recent advances in bioengineering, biorefining and catalysis. Angewandte Chemie (International Edition) 55(29):8164-8215.



3.    Grabber JH, Hatfield RD, Lu F, & Ralph J (2008) Coniferyl ferulate incorporation into lignin enhances the alkaline delignification and enzymatic degradation of maize cell walls. Biomacromolecules 9(9):2510-2516.



4.    Ralph J (2010) Hydroxycinnamates in lignification. Phytochemistry Reviews 9(1):65-83.



5.    Wilkerson CG, Mansfield SD, Lu F, Withers S, Park J-Y, Karlen SD, Gonzales-Vigil E, Padmakshan D, Unda F, Rencoret J, & Ralph J (2014) Monolignol ferulate transferase introduces chemically labile linkages into the lignin backbone. Science 344(6179):90-93.



6.    Karlen SD, Zhang C, Peck ML, Smith RA, Padmakshan D, Helmich KE, Free HCA, Lee S, Smith BG, Lu F, Sedbrook JC, Sibout R, Grabber JH, Runge TM, Mysore KS, Harris PJ, Bartley LE, & Ralph J (2016) Monolignol ferulate conjugates are naturally incorporated into plant lignins. Science Advances 2(10):e1600393.



7.    Smith RA, Gonzales-Vigil E, Karlen SD, Park J-Y, Lu F, Wilkerson CG, Samuels L, Mansfield SD, & Ralph J (2015) Engineering monolignol p-coumarate conjugates into Poplar and Arabidopsis lignins. Plant Physiology 169(4):2992-3001.



8.    Sibout R, Le Bris P, Legee F, Cezard L, Renault H, & Lapierre C (2016) Structural redesigning Arabidopsis lignins into alkali-soluble lignins through the expression of p-coumaroyl-CoA:monolignol transferase PMT. Plant Physiology 170(3):1358-1366.



9.    del Río JC, Rencoret J, Prinsen P, Martínez ÁT, Ralph J, & Gutiérrez A (2012) Structural characterization of wheat straw lignin as revealed by analytical pyrolysis, 2D-NMR, and reductive cleavage methods. Journal of Agricultural and Food ����vlog�ٷ���� 60(23):5922-5935.



10. Lan W, Lu F, Regner M, Zhu Y, Rencoret J, Ralph SA, Zakai UI, Morreel K, Boerjan W, & Ralph J (2015) Tricin, a flavonoid monomer in monocot lignification. Plant Physiology 167(4):1284-1295.



11. Lan W, Rencoret J, Lu F, Karlen SD, Smith BG, Harris PJ, del Rio JC, & Ralph J (2016) Tricin-lignins: Occurrence and quantitation of tricin in relation to phylogeny. The Plant Journal 88(6):1046-1057.



12. Lan W, Morreel K, Lu F, Rencoret J, del Rio JC, Voorend W, Vermerris W, Boerjan W, & Ralph J (2016) Maize tricin-oligolignol metabolites and their implications for monocot lignification. Plant Physiology 171(2):810-820.



13. Eloy NB, Voorend W, Lan W, Cesarino I, Vanholme R, de Lyra Soriano Saleme M, Goeminne G, Pallidis A, Morreel K, Nicomedes J, Ralph J, & Boerjan W (2017) Silencing chalcone synthase in maize impedes the incorporation of tricin into lignins and increases lignin content. Plant Physiology 173:998-1016.